True relationship between bones/armature and rigginh
Vertex movements are referred to the head bone, tail position is important only in case of automatic weighting or bone heat weighting, and - of course - in case of IK chain or other connected bones.

After weighting is done, if your bone isn't parent connected with another bone, you can freely move the tail in edit mode (i.e. to align axes with world axes) without affecting the behaviour of the rig.